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- EMDB-3577: MTA2-RBBP7 complex -

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Basic information

Entry
Database: EMDB / ID: 3577
TitleMTA2-RBBP7 complex
Map data
SampleMTA2-RBBP7 complex:
SourceHomo sapiens (human)
Methodsingle particle reconstruction / 38 Å resolution
AuthorsBrasen C / Dorosz J / Wiuf A / Boesen T / Mirza O / Gajhede M
CitationJournal: Biochim. Biophys. Acta / Year: 2017
Title: Expression, purification and characterization of the human MTA2-RBBP7 complex.
Authors: Christoffer Brasen / Jerzy Dorosz / Anders Wiuf / Thomas Boesen / Osman Mirza / Michael Gajhede
Abstract: The repressive Nucleosome Remodeling and histone Deacetylation (NuRD) complex remodels the chromatin structure by coupling ATP-dependent remodeling activity with histone deacetylase function and ...The repressive Nucleosome Remodeling and histone Deacetylation (NuRD) complex remodels the chromatin structure by coupling ATP-dependent remodeling activity with histone deacetylase function and plays important roles in regulating gene transcription, DNA damage repair and chromatin assembly. The complex is composed of six subunits: Metastasis Associated proteins MTA1/2/3 initially recruit histone chaperones RBBP4/7 followed by the histone deacetylases HDAC1/2 forming a core complex. Further association of the CpG-binding protein MBD2/3, p66α/β and the ATP-dependent helicase CDH3/4 constitutes the NuRD complex. Recent structural studies on truncated human proteins or orthologous have revealed that the stoichiometry of the MTA1-RBBP4 complex is 2:4. This study reports expression and purification of the intact human MTA2-RBBP7 complex using HEK293F cells as expression system. In analogy with findings on the Drosophila NuRD complex, we find that also the human MTA-RBBP can be isolated in vitro. Taken together with previous findings this suggests, that MTA-RBBP is a stable complex, with a central role in the initial assembly of the human NuRD complex. Refined 3D volumes of the complex generated from negative stain electron microscopy (EM) data reveals an elongated architecture that is capable of hinge like motion around the center of the particle.
DateDeposition: Jan 17, 2017 / Header (metadata) release: Feb 15, 2017 / Map release: May 3, 2017 / Last update: May 3, 2017

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.02
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.02
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_3577.map.gz (map file in CCP4 format, 19653 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
170 pix
3.15 Å/pix.
= 535.5 Å
170 pix
3.15 Å/pix.
= 535.5 Å
170 pix
3.15 Å/pix.
= 535.5 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 3.15 Å
Density
Contour Level:0.005 (by emdb), 0.02 (movie #1):
Minimum - Maximum-0.032571185 - 0.10222287
Average (Standard dev.)0.00017141107 (0.0044833473)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions170170170
Origin000
Limit169169169
Spacing170170170
CellA=B=C: 535.5 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z3.153.153.15
M x/y/z170170170
origin x/y/z0.0000.0000.000
length x/y/z535.500535.500535.500
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS170170170
D min/max/mean-0.0330.1020.000

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Supplemental data

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Sample components

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Entire MTA2-RBBP7 complex

EntireName: MTA2-RBBP7 complex / Number of components: 1

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Component #1: protein, MTA2-RBBP7 complex

ProteinName: MTA2-RBBP7 complex / Recombinant expression: No
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human) / Vector: pOPINHALO7/pOPINF / Cell of expression system: HEK293F

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle
Sample solutionpH: 7.5
VitrificationCryogen name: NONE

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Electron microscopy imaging

Experimental equipment
Model: Tecnai Spirit / Image courtesy: FEI Company
ImagingMicroscope: FEI TECNAI SPIRIT
Electron gunElectron source: LAB6 / Accelerating voltage: 120 kV / Electron dose: 10 e/Å2 / Illumination mode: OTHER
LensCs: 2.2 mm / Imaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: TVIPS TEMCAM-F416 (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 1267
3D reconstructionResolution: 38 Å / Resolution method: FSC 0.143 CUT-OFF

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